Fig. 1

Four different ways to record location and species of mRNA transcripts. Transcripts can be imaged directly in intact tissue by hybridization to fluorophore-labelled probes, or their locations can be recorded before they are extracted and undergo NGS. Transcript species can be imaged repeatedly with the same probes but different fluorophores to create a gene-specific barcode as in ISH. Short probes can also be imaged to read along an amplified transcript and determine its sequence as in ISS. Arrays of spatially barcoded probes can be used to label mRNAs with a sequence indicating location before undergoing NGS. Finally, cells or regions of interest can be directly microdissected and their locations recorded before their transcriptomes undergo NGS. Created with biorender.com